[BioC] target file and error message

[Wolfgang Huber]

Dear Chintanu,

the target file can be (needs to be) produced by you, it is a way of
telling the various subsequent analysis methods which biological samples
were on which array, which colour etc.

Regarding installation, please do follow the instructions at
http://www.bioconductor.org/download

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


Chintanu scripsit:
> Hi All,
> 
> I'm a novice both to R and microarray, and am struggling to learn both by
> myself.  Currently, I have got a microarray dataset from a research lab
> which contains cDNA and Affymetrix data files. The R-based literature refers
> many times to a file that contains target description (a .txt file with
> names like target.txt). But my dataset interestingly doesn't have any of
> such files. I am now struggling to find out how important this .txt file is
> as otherwise I have all the relevant image processing output files (e.g.,
> .gpr file). From the literature, I do understand that the so-called 'target
> file' contains information about the RNA samples used as targets in the
> microarray experiment, yet I'm wondering whether such files may be created
> at one's end too. Or, is it ONLY the relevant lab which can give me this
> file and else I can't move ahead!
> 
> 
> 
> However, I do see that there is an information file in the dataset which
> talks about the patient's name, file name and so on, but somehow I am
> pessimistic that this is the file I am looking for (a part of it is attached
> below).
> 
> 
> 
> Patients   File         Cy5                Cy3
> Gal_File
>                    GenePix            Notes
> 
> PreB1     B1a         Test               Control Pool
> HS_10.5K_GP.gal
> Pro 3.0
> 
>               B1b         Test               Control Pool
> HS_10.5K_GP.gal                 Pro 3.0
> 
>               B1cDS    Control Pool     Test
> HS_10.5K_GP.gal                 Pro 3.0             Dye Swap
> 
> PreB2    B2a         Test                Control Pool
> HS_10.5K_GP.gal
> Pro 3.0
> 
>              B2b         Test                Control Pool
> PMCI_10.5KSC_GP.gal         Pro 3.0
> 
>              B2cDS    Control Pool     Test
> HS_10.5K_GP.gal                 Pro 3.0             Dye Swap
> 
> 
> 
> 
> *Part 2*:
> 
> I'm also struggling to figure out why I get error messages, as below, while
> loading certain packages and whether there is a way to correct this problem
> .
> 
> 
> library(marrayPlots)
> Error in library(marrayPlots) :
> 'marrayPlots' is not a valid package -- installed < 2.0.0?
> 
> 
> 
> library(marrayNorm)
> Error in library(marrayNorm) :
> 'marrayNorm' is not a valid package -- installed < 2.0.0?
> 
> 
> May I request you to kindly reply and help me out, please !
> 
> Cheers,
> 
> Chintanu
> 
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